Transcriptomic Analysis of the Sulfate Starvation Response of Pseudomonas aeruginosa

ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that causes a number of infections in humans, but is best known for its association with cystic fibrosis. It is able to use a wide range of sulfur compounds as sources of sulfur for growth. Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as the sulfur source led not only to a sulfate starvation response but also to induction of genes involved with type III secretion systems.

[1]  Richard D Cummings,et al.  Altered O-glycosylation and sulfation of airway mucins associated with cystic fibrosis. , 2005, Glycobiology.

[2]  B. Tümmler,et al.  The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[3]  N. M. Kredich,et al.  Hydroxyl radical footprints and half-site arrangements of binding sites for the CysB transcriptional activator of Salmonella typhimurium , 1995, Journal of bacteriology.

[4]  R. Ramphal,et al.  Pseudomonas aeruginosa outer membrane adhesins for human respiratory mucus glycoproteins , 1994, Infection and immunity.

[5]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[6]  T. Leisinger,et al.  The assimilation of sulfur from multiple sources and its correlation with expression of the sulfate-starvation-induced stimulon in Pseudomonas putida S-313. , 1996, Microbiology.

[7]  Michael I. Jordan,et al.  Sulfur and Nitrogen Limitation in Escherichia coli K-12: Specific Homeostatic Responses , 2005, Journal of bacteriology.

[8]  U. Römling,et al.  Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. , 2005, Journal of medical microbiology.

[9]  J. Mattick,et al.  tonB3 Is Required for Normal Twitching Motility and Extracellular Assembly of Type IV Pili , 2004, Journal of bacteriology.

[10]  S. Lory,et al.  Complete genome sequence of Pseudomonas aeruginosa PAO 1 , an opportunistic pathogen , 2000 .

[11]  J. Lo-Guidice,et al.  Human airway mucin glycosylation: A combinatory of carbohydrate determinants which vary in cystic fibrosis , 2001, Glycoconjugate Journal.

[12]  T. Leisinger,et al.  Involvement of CysB and Cbl regulatory proteins in expression of the tauABCD operon and other sulfate starvation-inducible genes in Escherichia coli , 1997, Journal of bacteriology.

[13]  Peter F. Hallin,et al.  Comparative Genomics of Four Pseudomonas Species , 2004 .

[14]  J. Lyczak,et al.  Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist. , 2000, Microbes and infection.

[15]  M. Kertesz,et al.  Genetic organization of sulphur‐controlled aryl desulphonation in Pseudomonas putida S‐313 , 1999, Molecular microbiology.

[16]  R. Koebnik TonB-dependent trans-envelope signalling: the exception or the rule? , 2005, Trends in microbiology.

[17]  Michael I. Jordan,et al.  Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[18]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[19]  J. Ramos Genomics, life style and molecular architecture , 2004 .

[20]  P. Cornelis,et al.  Diversity of siderophore-mediated iron uptake systems in fluorescent pseudomonads: not only pyoverdines. , 2002, Environmental microbiology.

[21]  J. Helmann The extracytoplasmic function (ECF) sigma factors. , 2002, Advances in microbial physiology.

[22]  S. Lory,et al.  Isolation and characterization of Pseudomonas aeruginosa genes inducible by respiratory mucus derived from cystic fibrosis patients , 1996, Molecular microbiology.

[23]  C. Hart,et al.  Use of suppression subtractive hybridization to examine the accessory genome of the Liverpool cystic fibrosis epidemic strain of Pseudomonas aeruginosa. , 2006, Journal of medical microbiology.

[24]  Lei Xi,et al.  Molecular mechanisms of biocatalytic desulfurization of fossil fuels , 1996, Nature Biotechnology.

[25]  J. Rhodes,et al.  Increasing the intra-Golgi pH of cultured LS174T goblet-differentiated cells mimics the decreased mucin sulfation and increased Thomsen-Friedenreich antigen (Gal beta1-3GalNac alpha-) expression seen in colon cancer. , 2001, Glycobiology.

[26]  M. Kertesz Metabolism of Sulphur-Containing Organic Compounds , 2004 .

[27]  T. Omori,et al.  The σ54‐dependent transcriptional activator SfnR regulates the expression of the Pseudomonas putida sfnFG operon responsible for dimethyl sulphone utilization , 2004, Molecular microbiology.

[28]  H. Tsai,et al.  Production of mucin degrading sulphatase and glycosidases by Bacteroides thetaiotaomicron , 1991 .

[29]  R. Iwanicka-Nowicka,et al.  The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5′‐phosphosulphate (APS) as a signalling molecule for sulphate excess , 2002, Molecular microbiology.

[30]  J. Oakeshott,et al.  A global response to sulfur starvation in Pseudomonas putida and its relationship to the expression of low-sulfur-content proteins. , 2007, FEMS microbiology letters.

[31]  Gerald B. Pier,et al.  Lung Infections Associated with Cystic Fibrosis , 2002, Clinical Microbiology Reviews.

[32]  J. Ramos Biosynthesis of macromolecules and molecular metabolism , 2004 .

[33]  R. Carubelli,et al.  Respiratory mucous secretions in patients with cystic fibrosis: relationship between levels of highly sulfated mucin component and severity of the disease. , 1983, Clinica chimica acta; international journal of clinical chemistry.

[34]  M. Quadroni,et al.  Analysis of global responses by protein and peptide fingerprinting of proteins isolated by two-dimensional gel electrophoresis. Application to the sulfate-starvation response of Escherichia coli. , 1996, European journal of biochemistry.

[35]  M. Kertesz Riding the sulfur cycle--metabolism of sulfonates and sulfate esters in gram-negative bacteria. , 2000, FEMS microbiology reviews.

[36]  T. Leisinger,et al.  The Escherichia coli ssuEADCB Gene Cluster Is Required for the Utilization of Sulfur from Aliphatic Sulfonates and Is Regulated by the Transcriptional Activator Cbl* , 1999, The Journal of Biological Chemistry.

[37]  M. Kertesz,et al.  A Novel Reduced Flavin Mononucleotide-Dependent Methanesulfonate Sulfonatase Encoded by the Sulfur-Regulatedmsu Operon of Pseudomonas aeruginosa , 1999, Journal of bacteriology.

[38]  T. Leisinger,et al.  The Sulfur-Regulated Arylsulfatase Gene Cluster ofPseudomonas aeruginosa, a New Member of thecys Regulon , 2000, Journal of bacteriology.

[39]  A Danchin,et al.  Sulphur islands in the Escherichia coli genome: markers of the cell's architecture? , 2000, FEBS letters.

[40]  T. Leisinger,et al.  Proteins induced by sulfate limitation in Escherichia coli, Pseudomonas putida, or Staphylococcus aureus , 1993, Journal of bacteriology.

[41]  R. Dixon,et al.  Domain Architectures of σ54-Dependent Transcriptional Activators , 2003 .

[42]  Sheng Zhong,et al.  ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis , 2003, Nucleic Acids Res..

[43]  S. Lory,et al.  The Genome of Pseudomonas aeruginosa , 2004 .

[44]  M. Schuster,et al.  The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing , 2004, Molecular microbiology.

[45]  J. Saunders,et al.  A novel mucin-sulphatase activity found in Burkholderia cepacia and Pseudomonas aeruginosa. , 1999, Journal of medical microbiology.

[46]  M. Pagni,et al.  The elusive roles of bacterial glutathione S-transferases: new lessons from genomes , 2002, Applied Microbiology and Biotechnology.

[47]  D. Ussery,et al.  Extracytoplasmic function sigma factors in Pseudomonas syringae. , 2005, Trends in microbiology.

[48]  S. Lory,et al.  Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen , 2000, Nature.

[49]  Rafael A. Irizarry,et al.  A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .

[50]  Qing Yang,et al.  Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  K. Poole,et al.  A second tonB gene in Pseudomonas aeruginosa is linked to the exbB and exbD genes. , 2000, FEMS microbiology letters.

[52]  A. Danchin,et al.  Global Expression Profile of Bacillus subtilis Grown in the Presence of Sulfate or Methionine , 2002, Journal of bacteriology.

[53]  V. Bhavanandan,et al.  Differential binding of Pseudomonas aeruginosa to normal and cystic fibrosis tracheobronchial mucins. , 1994, Glycobiology.

[54]  Maynard V. Olson,et al.  Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa , 2003, Journal of bacteriology.

[55]  J. Buer,et al.  Genome-Wide Transcriptional Profiling of the Steady-State Response of Pseudomonas aeruginosa to Hydrogen Peroxide , 2005, Journal of bacteriology.

[56]  A. M. Roberton,et al.  Bacterial glycosulphatases and sulphomucin degradation. , 1997, Canadian journal of gastroenterology = Journal canadien de gastroenterologie.

[57]  K. Waltersson,et al.  The crystal structure of Cs[VOF3] · 12H2O , 1979 .

[58]  M. Quadroni,et al.  Regulation of the sulfate starvation response in Pseudomonas aeruginosa: role of cysteine biosynthetic intermediates. , 1998, Microbiology.

[59]  J. Costerton,et al.  Production of mucoid microcolonies by Pseudomonas aeruginosa within infected lungs in cystic fibrosis , 1980, Infection and immunity.

[60]  L. P. Aristoteli,et al.  Mucin Degradation Mechanisms by Distinct Pseudomonas aeruginosa Isolates In Vitro , 2003, Infection and Immunity.

[61]  M. Quadroni,et al.  Proteome mapping, mass spectrometric sequencing and reverse transcription-PCR for characterization of the sulfate starvation-induced response in Pseudomonas aeruginosa PAO1. , 1999, European journal of biochemistry.

[62]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[63]  Cheng Li,et al.  DNA-Chip Analyzer (dChip) , 2003 .